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MSMS man page
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<H3>MSMS(1)                   User Commands                   MSMS(1)</H3>
</pre>
<H2>NAME</H2>
<H3><pre>     msms v2.5<p></pre></H3>
 <p>
<DL>
<DT><H2>SYNOPSIS</H2>
<NOBR>
<DD><B>msms</B> [ <A href="#if">-if</A> filename ] [ <A href="#of">-of</A> filename ] [ <A href="#af">-af</A> filename ]<WBR>
     [ <A href="#pr">-probe_radius</A> radius ] [ <A href="#de">-density</A> density ] [ <A href="#noa">-no_area</A> ]<WBR>
     [ <A href="#su">-surface</A> &lt;tses,ases&gt; ] [ <A href="#so">-socket</A> servicename ] [ <A href="#si">-sinetd</A> ]<WBR>
     [ <A href="#noh">-noh</A> ] [ <A href="#nor1">-no_rest_on_pbr</A> ] [ <A href="#nor2">-no_rest ] [ <A href="#fr">-free_vertices</A> ]<WBR>
     [ <A href="#al">-all_components</A> ] [ <A href="#on">-one_cavity</A> #atoms at1 [at2] [at3] ]<WBR>
     [ <A href="#nohead">-no_header</A> ]<WBR>
</NOBR>

<DT><H2>DESCRIPTION</H2>
<DD> MSMS computes, for a given set of  spheres  S  and  a  probe
     radius  rp , the Reduced Surface and the analytical model of
     the Solvent Excluded Surface ( SES ). The SES  can  then  be
     triangulated with a given vertex density.<p>
     The program can run  in  standalone  or  server  mode   - if
     filename ). In server mode, the only requested option is the
     socket name to be used to communicate with the client appli
     cation ( -socket servicename or -sinetd ).

<DT><H2>OPTIONS</H2>
<DT> Options may appear in any order and may be  abbreviated.  If
     the  abbreviation  matches  several options, the first match
     will be used.<p>
<DL>

<DT><B><I><a name="if"> -if filename </a></B></I><br>
<DD>      Allows to specify the file from which the sphere set  S
          will  be  read. This file contains the center ( x,y,z )
          and the radius r of one sphere per line.  These  number
          are  stored  in  a free format. Empty lines  and  Lines
	  starting with the character `#' are treated as comments 
	  and are  skipped.   The  radius  can  be followed by an 
	  optional atom name (string). This name, if present, will
	  be  appended to  the  vertices in the  surface  and area 
	  output files  (see the new pdb_to_xyzrn script that adds 
	  atom names from pdb file).
          This  option  is the only requested option when MSMS is
          run in standalone mode.<p>

<DT><B><I><a name="of"> -of filename </a></B></I><br>
<DD>      Allows to specify the files in which to store the  tri
          angulated  solvent  excluded  surface  resulting from a
          calculation. Two files will be created,  one  for  ver
          tices  and one for faces. If the component number is 0,
          files  called  filename.vert  and   filename.face   are
          created.  For other components, the component number is
          inserted in the file name, for  example  for  the  com
          ponent  number  3  the files are called filename_3.vert
          and filename_3.face.<br>
          The face file contains three header lines  followed  by
          one triangle per line. The first header line provides a
          comment and the file name of the sphere set. The second
          header  line  holds  comments  about the content of the
          third line. The third header line provides  the  number
          of  triangles,  the  number  of spheres in the set, the
          triangulation density and the probe sphere radius.  The
          first  three  numbers are (1 based) vertex indices. The
          next field can be: 1 for a triangle in  a  toric  reen
          trant  face,  2  for  a triangle in a spheric reentrant
          face and 3 for a triangle in a contact face.  The  last
          number  on the line is the (1 based) face number in the
          analytical description of the solvent excluded surface.
          These  values  are written in the following format ``%6d
          %6d %6d %2d %6d''.<br>
          The vertex file contains three header lines (similar to
          the  header  in  the .face file) followed by one vertex
          per line and provides the coordinates (x,y,z)  and  the
          normals  (nx,ny,nz)  followed by the number of the face
          (in the analytical description of the solvent  excluded
          surface)  to  which the vertex belongs. The vertices of
          the analytical surface have a value 0 in that field and
          the  vertices lying on edges of this surface have nega
          tive values. The next field holds the (1  based)  index
          of the closest sphere. The next field is 1 for vertices
          which belong to toric reentrant faces  (including  ver
          tices of the analytical surface), 2 for vertices inside
          reentrant faces  and  3  for  vertices  inside  contact
          faces.  Finally, if atom names were present in the input 
	  file, the name of the  closest atom is  written for each 
	  vertex. These values are written in the following format
          ``%9.3f %9.3f %9.3f %9.3f %9.3f %9.3f %7d %7d %2d %s''.<p>

<DT><B><I><a name="af"> -af filename</a></B></I><br>
<DD>      Allows to specify the name of the file  used  to  store
          solvent  excluded and solvent accessible surface areas.
          The surface areas in each surface component are  listed
          for every atom.<p>

<DT><B><I><a name="nohead"> -no_header</a></B></I><br>
<DD>      By default a 3 lines header is written into  the  .face
          and  .vert  files.  This  flags  allows no to write out
          these headers.<p>

<DT><B><I><a name="pr"> -probe_radius radius</a></B></I><br>
<DD>      Used to modify the default value of  the  probe  sphere
          radius (1.5 Angstrom). No check is done on the validity
          of the probe radius. MSMS will fail to compute the tri
          angulation template sphere for radii that are too small
          or too large. Values ranging from 0.5 to 10 should pose
          no problem.<p>

<DT><B><I><a name="de"> -density density</a></B></I><br>
<DD>      Used to modify the default triangulation  density  (1.0
          vertex/Angstrom^2).  No test is done on the validity of
          this  parameter.  Typical  values  are  1.0  for  large
          molecules (&gt;1000 atoms) and 3.0 for smaller molecules.

<DT><B><I><a name="noa"> -no_area</a></B></I><br>
<DD>      This option allows to turn off the surface area  compu
          tation.

<DT><B><I><a name="su"> -surface &lt;tses,ases&gt;</a></B></I><br>
<DD>      Used to specify which  surface  to  calculate.  At  the
          moment,  the  only choices are I. tses for triangulated
          solvent excluded surface and ases for  analytical  sol
          vent  excluded  surface. By default the surface is tri
          angulated. This option is mainly used to avoid triangu
          lation,  for  instance,  when one is interested only in
          surface areas.<p>

<DT><B><I><a name="so"> -socket servicename</a></B></I><br>
<DD>      When MSMS is started  with  this  option,  the  program
          enters  the  server mode and ``listens'' to the specified
          Unix domain socket for clients requesting this service.
          If  a  client program requests this service the connec
          tion is established and MSMS expects to get the  compu
          tation  parameters and the spheres from the client thru
          this socket. Once the  calculation  is  completed  MSMS
          will  send  the triangulated surface to the client over
          this socket. This option doesn't use a general  way  to
          encode  values  (like  xdr) and works only on a limited
          set of architectures.<p>

<DT><B><I><a name="si"> -sinetd</a></B></I><br>
<DD>      This option is used to put MSMS in the server mode when
          MSMS  is  started  by  the internet daemon. This allows
          MSMS to be started whenever a client  program  requests
          MSMS to run.<p>

<DT><B><I><a name="noh"> -noh</a></B></I><br>
<DD>      Used to skip atoms with radius 1.2...???? (I know !)<p>

<DT><B><I><a name="nor1"> -no_rest_on_pbr</a></B></I><br>
<DD>      Because of badly handled singular  cases  or  numerical
          instability,  it can happen that MSMS has problems tri
          angulating the surface. By default,  the  program  will
          restart   the  computation  up  to  five  times,  after
          increasing the radius of the atoms causing the  problem
          by  0.1  Angstrom.  This option prevents MSMS from res
          tarting the calculation if problems  occur  during  the
          triangulation of spherical reentrant faces (which often
          points to singularities problems). The  resulting  tri
          angulated surface won't be correct and might have holes
          (see also -no_rest).<p>

<DT><B><I><a name="nor2"> -no_rest</a></B></I><br>
<DD>      This option is used to prevent MSMS from restarting the
          computation in any case (see also -no_rest_on_pbr).<p>

<DT><B><I><a name="fr"> -free_vertices</a></B></I><br>
<DD>      By default, free vertices of the  reduced  surface  are
          not searched for. Use this option to force their detec
          tion.<p>

<DT><B><I><a name="al"> -all_components</a></B></I><br>
<DD>      By default, only the external component of the  molecu
          lar  surfaces  (reduced  and solvent excluded) are com
          puted. This option allows to force  MSMS  to  find  all
          components.  If  the  -of filename option is specified,
          files with extension .vert and .face  will  be  created
          for each component.<p>

<DT><B><I><a name="on"> -one_cavity #atoms at1 [at2] [at3]</a></B></I><br>
<DD>      With this option one can compute a  specific  component
          of  the  molecular  surfaces  by  indicating  1, 2 or 3
          atom(s) the probe should initially touch. The number of
          such  atoms is specified in followed by the correspond
          ing number of (0 based) atom indices.<p>
</DL>
</DL>

<H2>EXAMPLE</H2>
<DL>
<DD> Triangulate the solvent excluded surface of a set of spheres
     and saving the triangulation in myset.vert and myset.face :<p>
<DL><DD> msms -if myset.xyzr -of myset<p></DL>
<DD> Compute all components of the surfaces for a probe radius of
     1.4 and triangulate them with a density of 3.0:<p>
<DL><DD> msms -if myset.xyzr -de 3.0 -prob 1.4 -of myset<p></DL>
</DL>

<H2>FILES</H2>
<DL><DD> pdb_to_xyzr(1),<p></DL>

<H2>BUGS</H2>
<DL>
<DD> If all the vertices of a component of  the  reduced  surface
     also  belong  to  another component, MSMS fails to find this
     component. A work around is to specify the  first  face  for
     that component explicitly using the -one_cavity option.<p>
<DD> The genus of the reduced surface is sometimes wrong.<p>
<DD> Singular edges forming a full circles are not treated.<p>
<DD> Normal vectors of singular vertices point arbitrarily to the
     center of one of the probe they belong to.<p>
<DD> MSMS will crash or produce weird results if a sphere of S is
     entierly inside another sphere of S<p>
</DL>

<H2>AUTHOR</H2>
<DD>  Michel F. Sanner,
<DD>  The Scripps Research Institute, La Jolla, California.<p>

<p><hr>

<h5>Last Modified: 04:04pm PST, February 05, 1996</h5>
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